Last updated: 2018-09-17

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drug correlation analysis with target sets

method

  • scale the microarrary expression data for each sample to z-score accross all genes
  • do ssgsea on the converted microarray expression data
  • compute correlation scores for ssgsea score to the drug response data (IC50)

Result 1: drug correlation analysis with targets sets

pdf figure with dendogram

interactive figure without dendogram (same order)

interactive figure with target set class labels

interactive figure with regulator age labels

Result 2: the information on the cluster drugs

Target.s. Mechanism.of.action Class group
17-AAG HSP90 Heat Shock Protein 90 (hsp90) Inhibitor Other targeted therapies 1
AZD6244 MEK MEK1 and MEK2 Inhibitor Kinase inhibitor 1
PD-0325901 MEK MEK1 and MEK2 Inhibitor Kinase inhibitor 1
AEW541 IGF-1R IGF-1R Inhibitor Kinase inhibitor 2
Irinotecan Topoisomerase I NA NA 2
L-685458 Gamma Secretase gamma-Secretase Inhibitor Other targeted therapies 2
Nutlin-3 MDM2 MDM2 Inhibitor Other targeted therapies 2
Paclitaxel beta-tubulin Microtubule-Stabilizing Agents Cytotoxic 2
Panobinostat HDAC Histone Deacetylase (HDAC) Inhibitor Other targeted therapies 2
PF2341066 c-MET, ALK c-MET and ALK Inhibitor Kinase inhibitor 2
RAF265 Raf kinase B, KDR Raf kinase B and KDR Inhibitor Kinase inhibitor 2
Sorafenib Flt3, C-KIT, PDGFRbeta, RET, Raf kinase B, Raf kinase C, VEGFR-1, KDR, FLT4 Multi-kinase inhibitor Kinase inhibitor 2
TAE684 ALK ALK Inhibitor Kinase inhibitor 2
TKI258 EGFR, FGFR1, PDGFRbeta, VEGFR-1, KDR Multi-kinase inhibitor Kinase inhibitor 2
Topotecan Topoisomerase I DNA Topoisomerase I Inhibitor Cytotoxic 2
AZD0530 Src, Abl/Bcr-Abl, EGFR Src and Abl inhibitor Kinase inhibitor 3
Erlotinib EGFR EGFR Inhibitor Kinase inhibitor 3
Lapatinib EGFR, HER2 EGFR and HER2 Inhibitor Kinase inhibitor 3
ZD-6474 Abl, EGFR, Flt3, C-KIT, RET, VEGFR-1, KDR, FLT4 Multi-kinase inhibitor Kinase inhibitor 3
LBW242 IAP Inhibitor of Apoptosis Proteins (IAP) Inhibitor Other targeted therapies 4
Nilotinib Abl/Bcr-Abl Abl Inhibitor Kinase inhibitor 4
PD-0332991 CDK4/6 CDK4/6 Inhibitor Kinase inhibitor 4
PHA-665752 c-MET c-MET Inhibitor Kinase inhibitor 4
PLX4720 RAF Raf kinase B Inhibitor Kinase inhibitor 5

Result 3: drug response correlate with goslim

Expand here to see past versions of drugheatmap_goslim.pdf:
Version Author Date
c1d5012 bingrus 2018-09-10

interactive plot

Target.s. Mechanism.of.action Class group
17-AAG HSP90 Heat Shock Protein 90 (hsp90) Inhibitor Other targeted therapies 1
AZD0530 Src, Abl/Bcr-Abl, EGFR Src and Abl inhibitor Kinase inhibitor 1
AZD6244 MEK MEK1 and MEK2 Inhibitor Kinase inhibitor 1
Erlotinib EGFR EGFR Inhibitor Kinase inhibitor 1
Lapatinib EGFR, HER2 EGFR and HER2 Inhibitor Kinase inhibitor 1
PD-0325901 MEK MEK1 and MEK2 Inhibitor Kinase inhibitor 1
ZD-6474 Abl, EGFR, Flt3, C-KIT, RET, VEGFR-1, KDR, FLT4 Multi-kinase inhibitor Kinase inhibitor 1
AEW541 IGF-1R IGF-1R Inhibitor Kinase inhibitor 2
Nilotinib Abl/Bcr-Abl Abl Inhibitor Kinase inhibitor 2
PD-0332991 CDK4/6 CDK4/6 Inhibitor Kinase inhibitor 2
PHA-665752 c-MET c-MET Inhibitor Kinase inhibitor 2
RAF265 Raf kinase B, KDR Raf kinase B and KDR Inhibitor Kinase inhibitor 2
Irinotecan Topoisomerase I NA NA 3
Topotecan Topoisomerase I DNA Topoisomerase I Inhibitor Cytotoxic 3
L-685458 Gamma Secretase gamma-Secretase Inhibitor Other targeted therapies 4
Nutlin-3 MDM2 MDM2 Inhibitor Other targeted therapies 4
Paclitaxel beta-tubulin Microtubule-Stabilizing Agents Cytotoxic 4
Panobinostat HDAC Histone Deacetylase (HDAC) Inhibitor Other targeted therapies 4
PF2341066 c-MET, ALK c-MET and ALK Inhibitor Kinase inhibitor 4
Sorafenib Flt3, C-KIT, PDGFRbeta, RET, Raf kinase B, Raf kinase C, VEGFR-1, KDR, FLT4 Multi-kinase inhibitor Kinase inhibitor 4
TAE684 ALK ALK Inhibitor Kinase inhibitor 4
TKI258 EGFR, FGFR1, PDGFRbeta, VEGFR-1, KDR Multi-kinase inhibitor Kinase inhibitor 4
LBW242 IAP Inhibitor of Apoptosis Proteins (IAP) Inhibitor Other targeted therapies 5
PLX4720 RAF Raf kinase B Inhibitor Kinase inhibitor 5

Session information

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] org.Hs.eg.db_3.6.0   kableExtra_0.9.0     knitr_1.20          
 [4] GSEABase_1.42.0      graph_1.58.0         annotate_1.58.0     
 [7] XML_3.98-1.16        AnnotationDbi_1.42.1 IRanges_2.14.11     
[10] S4Vectors_0.18.3     GSVA_1.28.0          heatmaply_0.15.2    
[13] viridis_0.5.1        viridisLite_0.3.0    plotly_4.8.0        
[16] ggplot2_3.0.0        dplyr_0.7.6          gplots_3.0.1        
[19] GEOquery_2.48.0      Biobase_2.40.0       BiocGenerics_0.26.0 
[22] reshape_0.8.7       

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2    class_7.3-14        modeltools_0.2-22  
  [4] mclust_5.4.1        rprojroot_1.3-2     rstudioapi_0.7     
  [7] flexmix_2.3-14      bit64_0.9-7         mvtnorm_1.0-8      
 [10] xml2_1.2.0          codetools_0.2-15    R.methodsS3_1.7.1  
 [13] robustbase_0.93-2   geneplotter_1.58.0  shinythemes_1.1.1  
 [16] jsonlite_1.5        workflowr_1.1.1     cluster_2.0.7-1    
 [19] kernlab_0.9-27      R.oo_1.22.0         shiny_1.1.0        
 [22] readr_1.1.1         compiler_3.5.0      httr_1.3.1         
 [25] backports_1.1.2     assertthat_0.2.0    lazyeval_0.2.1     
 [28] limma_3.36.3        later_0.7.3         htmltools_0.3.6    
 [31] tools_3.5.0         bindrcpp_0.2.2      gtable_0.2.0       
 [34] glue_1.3.0          reshape2_1.4.3      Rcpp_0.12.18       
 [37] trimcluster_0.1-2.1 gdata_2.18.0        crosstalk_1.0.0    
 [40] iterators_1.0.10    fpc_2.1-11.1        stringr_1.3.1      
 [43] rvest_0.3.2         mime_0.5            gtools_3.8.1       
 [46] dendextend_1.8.0    DEoptimR_1.0-8      MASS_7.3-50        
 [49] scales_1.0.0        TSP_1.1-6           hms_0.4.2          
 [52] promises_1.0.1      RColorBrewer_1.1-2  yaml_2.2.0         
 [55] memoise_1.1.0       gridExtra_2.3       stringi_1.2.4      
 [58] RSQLite_2.1.1       highr_0.7           gclus_1.3.1        
 [61] foreach_1.4.4       seriation_1.2-3     caTools_1.17.1.1   
 [64] rlang_0.2.2         pkgconfig_2.0.2     prabclus_2.2-6     
 [67] bitops_1.0-6        evaluate_0.11       lattice_0.20-35    
 [70] purrr_0.2.5         bindr_0.1.1         labeling_0.3       
 [73] htmlwidgets_1.2     bit_1.1-14          tidyselect_0.2.4   
 [76] plyr_1.8.4          magrittr_1.5        R6_2.2.2           
 [79] DBI_1.0.0           pillar_1.3.0        whisker_0.3-2      
 [82] withr_2.1.2         RCurl_1.95-4.11     nnet_7.3-12        
 [85] tibble_1.4.2        crayon_1.3.4        KernSmooth_2.23-15 
 [88] rmarkdown_1.10      grid_3.5.0          data.table_1.11.4  
 [91] blob_1.1.1          git2r_0.23.0        digest_0.6.16      
 [94] diptest_0.75-7      webshot_0.5.0       xtable_1.8-3       
 [97] tidyr_0.8.1         httpuv_1.4.5        R.utils_2.7.0      
[100] munsell_0.5.0       registry_0.5       

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